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Calcium in PDB 5eq2: Crystal Structure of the Srpa Adhesin From Streptococcus Sanguinis

Protein crystallography data

The structure of Crystal Structure of the Srpa Adhesin From Streptococcus Sanguinis, PDB code: 5eq2 was solved by L.V.Loukachevitch, K.M.Mcculloch, K.R.Vann, Z.Wawrzak, S.Anderson, T.M.Iverson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.56 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 174.522, 46.769, 64.761, 90.00, 102.72, 90.00
R / Rfree (%) 17.5 / 20.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Srpa Adhesin From Streptococcus Sanguinis (pdb code 5eq2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Crystal Structure of the Srpa Adhesin From Streptococcus Sanguinis, PDB code: 5eq2:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 5eq2

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Calcium binding site 1 out of 7 in the Crystal Structure of the Srpa Adhesin From Streptococcus Sanguinis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Srpa Adhesin From Streptococcus Sanguinis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:20.1
occ:1.00
 O B:HOH643 2.3 33.3 1.0
O A:HOH689 2.4 32.4 1.0
OE1 B:GLU400 2.4 24.0 1.0
OE1 A:GLU400 2.5 21.3 1.0
OE2 A:GLU400 2.5 21.8 1.0
OE2 B:GLU400 2.5 21.7 1.0
O B:HOH664 2.6 18.7 1.0
O A:HOH667 2.6 17.7 1.0
CD B:GLU400 2.8 20.5 1.0
CD A:GLU400 2.8 19.6 1.0
NH1 B:ARG415 4.2 18.5 1.0
O B:HOH722 4.2 19.9 1.0
CG B:GLU400 4.3 18.8 1.0
NH1 A:ARG415 4.4 19.3 1.0
O B:HOH707 4.4 22.2 1.0
CG A:GLU400 4.4 20.3 1.0
O A:HOH744 4.4 20.4 1.0
NH2 B:ARG415 4.5 16.6 1.0
NH2 A:ARG415 4.5 18.1 1.0
CZ B:ARG415 4.6 18.6 1.0
O B:ILE416 4.6 19.4 1.0
O A:ILE416 4.7 18.9 1.0
CZ A:ARG415 4.7 18.8 1.0
O B:HOH675 4.9 28.5 1.0
O A:HOH679 4.9 26.1 1.0

Calcium binding site 2 out of 7 in 5eq2

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Calcium binding site 2 out of 7 in the Crystal Structure of the Srpa Adhesin From Streptococcus Sanguinis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Srpa Adhesin From Streptococcus Sanguinis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:14.9
occ:1.00
 O A:THR255 2.2 14.4 1.0
OD1 A:ASP282 2.3 23.4 1.0
OD2 A:ASP353 2.3 15.8 1.0
OD1 A:ASP253 2.4 15.5 1.0
OD2 A:ASP281 2.5 13.4 1.0
OD1 A:ASP281 2.5 12.3 1.0
OD2 A:ASP253 2.5 17.0 1.0
CG A:ASP281 2.8 13.7 1.0
CG A:ASP253 2.8 16.5 1.0
CG A:ASP353 3.4 16.5 1.0
C A:THR255 3.5 13.6 1.0
CG A:ASP282 3.5 27.9 1.0
CB A:ASP353 3.9 14.4 1.0
OD2 A:ASP282 4.1 28.5 1.0
O A:HOH729 4.1 26.7 1.0
ND2 A:ASN357 4.2 13.3 1.0
CA A:THR255 4.2 14.8 1.0
N A:THR255 4.3 15.5 1.0
O A:HOH708 4.3 12.3 0.5
N A:ASP282 4.3 16.1 1.0
CB A:ASP253 4.3 21.1 1.0
CB A:ASP281 4.3 14.1 1.0
N A:SER283 4.4 18.3 1.0
CB A:THR255 4.4 15.3 1.0
N A:PRO256 4.4 11.8 1.0
CA A:PRO256 4.5 10.3 1.0
C A:PRO256 4.5 12.1 1.0
OD1 A:ASP353 4.5 15.1 1.0
OG A:SER283 4.6 17.1 1.0
CB A:SER283 4.6 20.9 1.0
O A:PRO256 4.7 14.1 1.0
CB A:ASP282 4.8 21.3 1.0
N A:PRO257 4.9 11.0 1.0
CA A:ASP282 4.9 17.8 1.0
CB A:ASN357 5.0 11.6 1.0
C A:ASP281 5.0 14.4 1.0
CA A:ASP281 5.0 12.8 1.0

Calcium binding site 3 out of 7 in 5eq2

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Calcium binding site 3 out of 7 in the Crystal Structure of the Srpa Adhesin From Streptococcus Sanguinis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Srpa Adhesin From Streptococcus Sanguinis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:30.9
occ:1.00
 O A:ACT506 1.9 23.7 1.0
O A:TYR375 2.1 32.3 1.0
O A:THR372 2.4 31.3 1.0
OD1 A:ASP434 2.4 34.0 1.0
O A:HOH698 2.4 38.2 1.0
O A:HOH696 2.7 51.6 1.0
C A:ACT506 2.8 36.2 1.0
OXT A:ACT506 3.0 46.2 1.0
CG A:ASP434 3.1 31.2 1.0
OD2 A:ASP434 3.1 35.7 1.0
OG1 A:THR372 3.1 32.7 1.0
C A:TYR375 3.3 37.3 1.0
C A:THR372 3.4 32.2 1.0
CA A:THR372 3.9 28.3 1.0
CB A:THR372 4.1 30.2 1.0
CA A:ASN376 4.1 47.7 1.0
N A:ASN376 4.2 41.1 1.0
CD A:PRO377 4.2 42.5 1.0
CH3 A:ACT506 4.2 35.7 1.0
CA A:TYR375 4.4 36.0 1.0
N A:TYR375 4.4 39.3 1.0
OH A:TYR428 4.4 34.0 1.0
O A:HOH616 4.5 35.7 1.0
CB A:ASP434 4.6 22.8 1.0
N A:ASP373 4.6 31.0 1.0
CB A:TYR375 4.8 32.2 1.0
ND2 A:ASN376 4.9 69.0 1.0
CG2 A:THR372 4.9 30.8 1.0
CB A:ASN376 4.9 57.6 1.0
CE2 A:TYR428 4.9 24.8 1.0
CA A:ASP373 4.9 33.8 1.0

Calcium binding site 4 out of 7 in 5eq2

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Calcium binding site 4 out of 7 in the Crystal Structure of the Srpa Adhesin From Streptococcus Sanguinis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Srpa Adhesin From Streptococcus Sanguinis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:21.7
occ:1.00
 O B:THR255 2.2 19.3 1.0
OD2 B:ASP353 2.3 21.4 1.0
OD1 B:ASP282 2.4 32.7 1.0
OD1 B:ASP253 2.4 26.0 1.0
OD2 B:ASP253 2.4 23.5 1.0
OD2 B:ASP281 2.5 26.1 1.0
OD1 B:ASP281 2.5 20.9 1.0
CG B:ASP253 2.7 26.2 1.0
CG B:ASP281 2.9 24.8 1.0
C B:THR255 3.4 20.3 1.0
CG B:ASP353 3.4 19.3 1.0
CG B:ASP282 3.6 38.1 1.0
CB B:ASP353 4.0 17.8 1.0
OD2 B:ASP282 4.1 38.8 1.0
ND2 B:ASN357 4.1 21.9 1.0
N B:THR255 4.2 23.8 1.0
CA B:THR255 4.2 25.9 1.0
CB B:ASP253 4.3 27.5 1.0
N B:ASP282 4.3 22.1 1.0
N B:SER283 4.4 24.2 1.0
CB B:ASP281 4.4 20.7 1.0
N B:PRO256 4.4 22.3 1.0
CB B:THR255 4.4 32.5 1.0
C B:PRO256 4.4 20.5 1.0
O B:HOH748 4.5 26.9 1.0
CA B:PRO256 4.5 20.7 1.0
OD1 B:ASP353 4.5 19.0 1.0
O B:HOH733 4.6 30.8 1.0
CB B:SER283 4.6 25.7 1.0
OG B:SER283 4.6 22.3 1.0
O B:PRO256 4.7 21.7 1.0
CB B:ASP282 4.8 32.2 1.0
N B:PRO257 4.8 20.5 1.0
CB B:ASN357 4.9 22.4 1.0
CG B:ASN357 4.9 22.2 1.0
CA B:ASP282 5.0 29.1 1.0

Calcium binding site 5 out of 7 in 5eq2

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Calcium binding site 5 out of 7 in the Crystal Structure of the Srpa Adhesin From Streptococcus Sanguinis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of the Srpa Adhesin From Streptococcus Sanguinis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:32.9
occ:1.00
 O B:HOH715 2.3 28.1 1.0
O B:HOH731 2.3 38.5 1.0
O B:HOH855 2.4 50.9 1.0
O B:HOH700 2.5 41.2 1.0
O B:HOH646 2.5 24.0 1.0
O B:HOH799 2.6 52.1 1.0
OXT B:ACT506 2.8 43.3 1.0
C B:ACT506 3.8 45.3 1.0
O B:ACT506 4.0 56.0 1.0
ND2 B:ASN309 4.1 27.9 1.0
CB B:ASN320 4.3 36.5 1.0
O B:ASN315 4.4 24.0 1.0
O B:ASN320 4.5 24.4 1.0
CH3 B:ACT507 4.5 17.7 1.0
O B:GLY314 4.5 23.7 1.0
O B:HOH828 4.5 43.8 1.0
CA B:ASN315 4.7 20.3 1.0
O B:ACT507 4.7 37.6 1.0
C B:ASN315 4.8 21.1 1.0
O B:PRO321 4.8 21.3 1.0

Calcium binding site 6 out of 7 in 5eq2

Go back to Calcium Binding Sites List in 5eq2
Calcium binding site 6 out of 7 in the Crystal Structure of the Srpa Adhesin From Streptococcus Sanguinis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of the Srpa Adhesin From Streptococcus Sanguinis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:19.5
occ:1.00
 O B:THR372 2.3 21.6 1.0
O B:HOH761 2.3 28.3 1.0
O B:TYR375 2.3 22.8 1.0
OD2 B:ASP434 2.4 21.5 1.0
O B:HOH710 2.5 23.1 1.0
O B:HOH778 2.5 27.6 1.0
OD1 B:ASP434 2.5 23.4 1.0
OG1 B:THR372 2.8 24.7 1.0
CG B:ASP434 2.8 21.1 1.0
C B:THR372 3.4 18.9 1.0
C B:TYR375 3.6 22.7 1.0
CA B:THR372 3.8 19.8 1.0
CB B:THR372 3.9 20.6 1.0
CB B:ASP434 4.3 21.4 1.0
CA B:ASN376 4.4 20.2 1.0
N B:ASN376 4.4 20.8 1.0
O B:HOH626 4.4 37.1 1.0
N B:ASP373 4.5 20.3 1.0
O B:HOH752 4.6 44.7 1.0
CA B:TYR375 4.6 19.4 1.0
N B:TYR375 4.6 20.5 1.0
CD B:PRO377 4.7 30.8 1.0
O B:HOH783 4.7 46.6 1.0
CG2 B:THR372 4.7 20.1 1.0
OH B:TYR428 4.7 23.5 1.0
CA B:ASP373 4.9 24.7 1.0
OD1 B:ASN376 5.0 32.4 1.0
O B:HOH665 5.0 28.3 1.0
CE2 B:TYR428 5.0 17.9 1.0

Calcium binding site 7 out of 7 in 5eq2

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Calcium binding site 7 out of 7 in the Crystal Structure of the Srpa Adhesin From Streptococcus Sanguinis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of the Srpa Adhesin From Streptococcus Sanguinis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca504

b:36.3
occ:1.00
 O B:HOH693 2.3 40.8 1.0
O B:ASP373 2.4 22.6 1.0
O B:HOH858 2.4 35.2 1.0
O B:HOH783 2.5 46.6 1.0
O B:HOH800 2.5 47.6 1.0
O B:HOH864 2.5 47.2 1.0
O B:HOH762 2.7 35.8 1.0
O B:HOH850 2.7 49.7 1.0
C B:ASP373 3.6 24.3 1.0
O B:HOH683 4.1 47.9 1.0
O B:HOH886 4.2 43.7 1.0
CA B:ASP373 4.3 24.7 1.0
O B:HOH778 4.3 27.6 1.0
O B:HOH819 4.3 20.3 0.5
N B:LYS374 4.6 19.9 1.0
CB B:ASP373 4.7 24.9 1.0
O B:LYS374 4.7 24.6 1.0
OH B:TYR268 4.8 22.8 1.0
CA B:LYS374 4.8 20.1 1.0
O B:HOH819 4.8 22.8 0.5

Reference:

B.A.Bensing, L.V.Loukachevitch, K.M.Mcculloch, H.Yu, K.R.Vann, Z.Wawrzak, S.Anderson, X.Chen, P.M.Sullam, T.M.Iverson. Structural Basis For Sialoglycan Binding By the Streptococcus Sanguinis Srpa Adhesin. J.Biol.Chem. V. 291 7230 2016.
ISSN: ESSN 1083-351X
PubMed: 26833566
DOI: 10.1074/JBC.M115.701425
Page generated: Sun Jul 14 18:41:13 2024

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